chr11-64895176-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015104.3(ATG2A):c.5614G>A(p.Val1872Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,612,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015104.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATG2A | ENST00000377264.8 | c.5614G>A | p.Val1872Met | missense_variant | Exon 41 of 41 | 1 | NM_015104.3 | ENSP00000366475.3 | ||
ATG2A | ENST00000418259.5 | c.5023G>A | p.Val1675Met | missense_variant | Exon 37 of 37 | 5 | ENSP00000413716.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460730Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 726642
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5614G>A (p.V1872M) alteration is located in exon 41 (coding exon 41) of the ATG2A gene. This alteration results from a G to A substitution at nucleotide position 5614, causing the valine (V) at amino acid position 1872 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at